{"gene":"RTN1","run_date":"2026-06-10T07:46:28","timeline":{"discoveries":[{"year":2015,"finding":"RTN1A interacts with PERK (an ER stress sensor) through its N-terminal and C-terminal domains; mutation of these domains prevents RTN1A-induced ER stress, establishing that RTN1A drives ER stress and apoptosis via direct physical interaction with PERK.","method":"Co-immunoprecipitation, domain deletion/mutation analysis, in vitro overexpression and knockdown with ER stress marker readouts","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal interaction mapping with domain mutants, in vivo knockdown rescue, replicated across cell and mouse models in a single rigorous study","pmids":["26227493"],"is_preprint":false},{"year":2017,"finding":"RTN1-C interacts with Bcl-xL and increases its localization in the ER, thereby reducing the anti-apoptotic activity of Bcl-xL and promoting mitochondria-associated apoptosis during ischemia/reperfusion injury.","method":"Co-immunoprecipitation, subcellular fractionation, RTN1-C overexpression/knockdown with apoptosis readouts in OGD/R and MCAO models","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus in vivo KD with defined phenotypic readout, single lab","pmids":["28981095"],"is_preprint":false},{"year":2007,"finding":"ER localization of RTN1-A is determined by its two long hydrophobic segments in the C-terminal domain; each hydrophobic segment is individually sufficient for ER targeting, and the length of the hydrophobic segment contributes to ER retention versus Golgi localization.","method":"EGFP fusion constructs with deletion mutants and truncations, fluorescence microscopy","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with systematic deletion mutants, single lab, two constructs tested","pmids":["17303085"],"is_preprint":false},{"year":2009,"finding":"The C-terminal region of RTN1-C (residues 186–208) contains a consensus sequence homologous to H4 histone and binds and condenses nucleic acids; this binding activity is regulated by an acetylation-deacetylation mechanism via HDAC8, which deacetylates an acetylated form of the RTN1-C C-terminal peptide.","method":"Electrophoretic mobility shift assay, NMR/fluorescence spectroscopy, kinetic enzyme assay with HDAC8 and acetylated synthetic peptide","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical assays with synthetic peptide and mutagenesis-equivalent acetylated form, single lab","pmids":["19140693"],"is_preprint":false},{"year":2010,"finding":"The RTN1-C C-terminal peptide (residues 186–208) binds copper and nickel ions via an ATCUN motif; the resulting metal-peptide complexes exhibit nuclease activity and, in acetylated form, inhibit HDAC activity at micromolar concentrations.","method":"UV-vis spectroscopy, kinetic nuclease assay, HDAC enzymatic inhibition assay with metal-peptide complexes","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assays with defined metal complexes and acetylated peptide, single lab replicate of prior finding","pmids":["20000484"],"is_preprint":false},{"year":2012,"finding":"The C-terminal region of RTN1-C contains a metal ion binding motif (HxE/D) capable of binding metal ions, suggesting metal binding contributes to formation of RTN multiprotein complexes.","method":"UV-vis spectroscopy, CD, multidimensional NMR spectroscopy, biological assays","journal":"Metallomics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, biophysical characterization without functional reconstitution of complex formation","pmids":["22522967"],"is_preprint":false},{"year":2014,"finding":"RTN1-C physically interacts with MANF (mesencephalic astrocyte-derived neurotrophic factor) in the ER; knockdown of RTN1-C reduces MANF localization in the ER.","method":"Yeast two-hybrid screen, GST pulldown, co-immunoprecipitation, immunofluorescence colocalization, RTN1-C knockdown","journal":"Acta biochimica et biophysica Sinica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interaction confirmed by orthogonal methods (Y2H, GST pulldown, Co-IP) plus localization consequence of KD, single lab","pmids":["25543119"],"is_preprint":false},{"year":2017,"finding":"RTN1 deficiency in mice shows no obvious effect on BACE1 activity because RTN3 compensates by elevation; however, RTN1 is preferentially localized to dendrites (especially Purkinje cell dendrites) rather than axons, differentiating its subcellular distribution from RTN3.","method":"RTN1-null mouse generation, immunofluorescence, BACE1 activity assay, Western blot","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct KO mouse with defined functional assay (BACE1 activity) and subcellular localization, single lab","pmids":["28733667"],"is_preprint":false},{"year":2018,"finding":"RTN1-C knockdown inhibits surface expression of mGluR5 (but not mGluR1) and attenuates intracellular Ca2+ release in MPP+-treated SN4741 cells; the protective effect of RTN1-C knockdown is partially reversed by mGluR5 activation, placing RTN1-C upstream of mGluR5-mediated Ca2+ homeostasis.","method":"siRNA knockdown, Western blot for surface mGluR5, Ca2+ imaging, pharmacological mGluR5 activation","journal":"Brain research bulletin","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KD combined with pharmacological rescue and Ca2+ imaging, single lab, two orthogonal readouts","pmids":["30521940"],"is_preprint":false},{"year":2018,"finding":"RTN1-C knockdown protects cortical neurons from traumatic injury by inhibiting mGluR1-mediated ER Ca2+ release and suppressing STIM1-related store-operated Ca2+ entry (SOCE), thereby attenuating intracellular Ca2+ overload.","method":"siRNA knockdown, Ca2+ imaging, Western blot for STIM1, thapsigargin-induced SOCE assay","journal":"Neurochemistry international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with Ca2+ imaging and molecular target (STIM1) identification, single lab, multiple readouts","pmids":["30352262"],"is_preprint":false},{"year":2021,"finding":"RTN1-C knockdown suppresses overactivated autophagy (reduced Beclin-1/PI-positive cells and autophagic protein expression) in ischemia/reperfusion injury models in vitro and in vivo, and reduces brain infarct volume after rapamycin treatment.","method":"Lentiviral shRNA knockdown, Western blot for autophagy markers, flow cytometry (Beclin-1/PI), MCAO rat model, rapamycin co-treatment","journal":"Acta biochimica et biophysica Sinica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo and in vitro KD with defined autophagy readouts, single lab","pmids":["33372676"],"is_preprint":false},{"year":2021,"finding":"In renal tubular epithelial cells under diabetic conditions, the transcription factor PU.1 binds the RTN1 promoter to drive RTN1 expression; lncRNA TUG1 inhibits PU.1 binding to the RTN1 promoter, thereby suppressing RTN1-mediated ER stress and apoptosis.","method":"Dual-luciferase reporter assay, RNA pulldown, RNA immunoprecipitation (RIP), chromatin immunoprecipitation (ChIP), adenoviral overexpression in vivo","journal":"Journal of leukocyte biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal chromatin and RNA interaction methods establishing transcriptional regulation of RTN1, single lab","pmids":["34062006"],"is_preprint":false}],"current_model":"RTN1 (particularly its RTN1-C isoform) is an ER-resident membrane protein anchored by two hydrophobic transmembrane segments; it promotes ER stress by directly interacting with the PERK kinase via its N- and C-terminal domains, interacts with Bcl-xL to sequester it in the ER and reduce its anti-apoptotic function, modulates intracellular Ca2+ homeostasis through mGluR1/mGluR5 and STIM1-mediated store-operated entry, regulates autophagy flux, binds nucleic acids and HDAC enzymes via a C-terminal histone H4-like motif subject to acetylation control, and interacts with MANF in the ER, collectively placing RTN1-C as a multifunctional ER scaffold that amplifies apoptotic and stress signals in neurons and renal cells."},"narrative":{"mechanistic_narrative":"RTN1 is an endoplasmic reticulum membrane protein that functions as a pro-apoptotic stress amplifier in neurons and renal cells, coupling ER stress sensing to apoptosis, calcium dysregulation, and autophagy [PMID:26227493, PMID:28981095, PMID:30521940]. Its ER localization is conferred by two long hydrophobic segments in the C-terminal domain, each individually sufficient for ER targeting, with segment length tuning ER retention versus Golgi distribution [PMID:17303085]. RTN1A drives ER stress and apoptosis by binding the ER stress sensor PERK through its N- and C-terminal domains, an interaction required for RTN1-induced stress signaling [PMID:26227493]. The RTN1-C isoform additionally engages the anti-apoptotic factor Bcl-xL, sequestering it in the ER to reduce its protective activity and promote mitochondria-associated apoptosis during ischemia/reperfusion [PMID:28981095], and it interacts with the ER protein MANF, controlling MANF's ER localization [PMID:25543119]. RTN1-C also governs intracellular Ca2+ homeostasis, acting upstream of mGluR5 surface expression and STIM1-mediated store-operated Ca2+ entry, such that its depletion attenuates Ca2+ overload and is protective in models of neuronal injury [PMID:30521940, PMID:30352262]. A C-terminal region (residues 186–208) bears a histone H4-like motif that binds and condenses nucleic acids under acetylation/deacetylation control by HDAC8 [PMID:19140693]. RTN1-C depletion further suppresses overactivated autophagy in ischemia/reperfusion injury [PMID:33372676], and RTN1 transcription is driven by PU.1 binding to its promoter, an event antagonized by lncRNA TUG1 to limit ER stress and apoptosis in diabetic renal tubular cells [PMID:34062006].","teleology":[{"year":2007,"claim":"Established what determines RTN1's subcellular address, showing the two C-terminal hydrophobic segments encode ER targeting and that segment length governs ER-versus-Golgi distribution.","evidence":"EGFP fusion constructs with deletion/truncation mutants analyzed by fluorescence microscopy","pmids":["17303085"],"confidence":"Medium","gaps":["Does not define a topology model for the full-length protein","Functional consequence of Golgi mislocalization untested"]},{"year":2009,"claim":"Identified a histone H4-like motif in the RTN1-C C-terminus that binds and condenses nucleic acids and is reversibly regulated by HDAC8-mediated deacetylation, suggesting a chromatin-linked activity beyond membrane functions.","evidence":"EMSA, NMR/fluorescence spectroscopy, and kinetic enzyme assay with HDAC8 and synthetic acetylated peptide","pmids":["19140693"],"confidence":"Medium","gaps":["In vitro peptide assays only; no demonstration of nuclear function in cells","Physiological nucleic acid targets unknown"]},{"year":2010,"claim":"Extended the C-terminal peptide characterization by showing it binds copper/nickel via an ATCUN motif, conferring nuclease activity and HDAC inhibition, linking metal coordination to its biochemical activities.","evidence":"UV-vis spectroscopy, kinetic nuclease assay, and HDAC inhibition assay with metal-peptide complexes","pmids":["20000484"],"confidence":"Medium","gaps":["In vitro only; cellular relevance of metal binding not shown","No reconstitution in full-length protein"]},{"year":2012,"claim":"Biophysically characterized an HxE/D metal ion binding motif in the C-terminal region as a potential mediator of RTN multiprotein complex formation.","evidence":"UV-vis, CD, and multidimensional NMR spectroscopy","pmids":["22522967"],"confidence":"Low","gaps":["No functional reconstitution of complex formation","Single-lab biophysical characterization without in vivo support"]},{"year":2014,"claim":"Defined an ER protein partner for RTN1-C by showing it physically interacts with MANF and controls MANF's ER localization, embedding RTN1-C in ER protein networks.","evidence":"Yeast two-hybrid, GST pulldown, Co-IP, immunofluorescence colocalization, and knockdown","pmids":["25543119"],"confidence":"Medium","gaps":["Functional consequence of the RTN1-C/MANF interaction unresolved","Single lab"]},{"year":2015,"claim":"Provided the central mechanism for RTN1-driven ER stress by mapping a direct PERK interaction to the N- and C-terminal domains and showing domain mutation abolishes RTN1-induced ER stress and apoptosis.","evidence":"Co-IP, domain deletion/mutation analysis, and overexpression/knockdown with ER stress readouts in cell and mouse models","pmids":["26227493"],"confidence":"High","gaps":["Whether RTN1 modulates the other ER stress arms (IRE1, ATF6) not addressed","Stoichiometry and structural basis of the PERK interaction unknown"]},{"year":2017,"claim":"Connected RTN1-C to mitochondrial apoptosis by showing it binds Bcl-xL and increases its ER localization, reducing its anti-apoptotic activity during ischemia/reperfusion.","evidence":"Co-IP, subcellular fractionation, and overexpression/knockdown with apoptosis readouts in OGD/R and MCAO models","pmids":["28981095"],"confidence":"Medium","gaps":["Direct versus indirect nature of Bcl-xL sequestration not fully resolved","Single lab"]},{"year":2017,"claim":"Distinguished RTN1 from its paralog RTN3 in vivo, showing RTN1 loss does not impair BACE1 activity due to RTN3 compensation and that RTN1 is preferentially dendritic.","evidence":"RTN1-null mouse, immunofluorescence, BACE1 activity assay, and Western blot","pmids":["28733667"],"confidence":"Medium","gaps":["Dendritic function of RTN1 not defined","Phenotype masked by RTN3 redundancy"]},{"year":2018,"claim":"Established RTN1-C as a regulator of neuronal Ca2+ homeostasis, placing it upstream of mGluR5 surface expression and STIM1-mediated store-operated Ca2+ entry, with knockdown protecting neurons from Ca2+ overload.","evidence":"siRNA knockdown, Ca2+ imaging, surface mGluR5/STIM1 Western blots, pharmacological mGluR5 activation, and thapsigargin SOCE assay in MPP+ and traumatic injury models","pmids":["30521940","30352262"],"confidence":"Medium","gaps":["Mechanism by which RTN1-C controls mGluR5 surface trafficking unknown","Receptor selectivity (mGluR5 vs mGluR1) across models not reconciled"]},{"year":2021,"claim":"Broadened RTN1-C's stress repertoire to autophagy, showing its knockdown suppresses overactivated autophagy and reduces infarct volume in ischemia/reperfusion models.","evidence":"Lentiviral shRNA knockdown, autophagy marker Western blots, flow cytometry, MCAO rat model with rapamycin co-treatment","pmids":["33372676"],"confidence":"Medium","gaps":["Molecular link between RTN1-C and the autophagy machinery undefined","Single lab"]},{"year":2021,"claim":"Defined transcriptional control of RTN1, showing PU.1 activates the RTN1 promoter and lncRNA TUG1 antagonizes this to suppress RTN1-mediated ER stress and apoptosis in diabetic renal tubular cells.","evidence":"Dual-luciferase reporter, RNA pulldown, RIP, ChIP, and adenoviral overexpression in vivo","pmids":["34062006"],"confidence":"Medium","gaps":["Whether this regulatory axis operates in neuronal tissues untested","Single lab"]},{"year":null,"claim":"How the membrane-anchored ER scaffold functions integrate with the C-terminal histone-like nucleic acid-binding/HDAC-modulating activity, and whether a single structural model reconciles RTN1's PERK, Bcl-xL, MANF, and Ca2+-regulatory roles, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No integrated structural model of full-length RTN1","Cellular role of the nucleic acid-binding/metal-binding C-terminal motif undemonstrated","Mechanistic unification of ER stress, Ca2+, and autophagy roles lacking"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[3]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[8,9]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1,2,6]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[0]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[1,11]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[10]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[11]}],"complexes":[],"partners":["PERK","BCL2L1","MANF","STIM1","HDAC8"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q16799","full_name":"Reticulon-1","aliases":["Neuroendocrine-specific protein"],"length_aa":776,"mass_kda":83.6,"function":"Inhibits amyloid precursor protein processing, probably by blocking BACE1 activity","subcellular_location":"Endoplasmic reticulum membrane; Golgi apparatus membrane","url":"https://www.uniprot.org/uniprotkb/Q16799/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RTN1","classification":"Not Classified","n_dependent_lines":4,"n_total_lines":1208,"dependency_fraction":0.0033112582781456954},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"RTN4","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RTN1","total_profiled":1310},"omim":[{"mim_id":"610243","title":"ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 27; ZFYVE27","url":"https://www.omim.org/entry/610243"},{"mim_id":"610236","title":"LUNAPARK; LNPK","url":"https://www.omim.org/entry/610236"},{"mim_id":"604277","title":"SPASTIN; SPAST","url":"https://www.omim.org/entry/604277"},{"mim_id":"604252","title":"BETA-SITE AMYLOID BETA A4 PRECURSOR PROTEIN-CLEAVING ENZYME 1; BACE1","url":"https://www.omim.org/entry/604252"},{"mim_id":"604249","title":"RETICULON 3; RTN3","url":"https://www.omim.org/entry/604249"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Endoplasmic reticulum","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":444.9}],"url":"https://www.proteinatlas.org/search/RTN1"},"hgnc":{"alias_symbol":[],"prev_symbol":["NSP"]},"alphafold":{"accession":"Q16799","domains":[{"cath_id":"1.20.5","chopping":"667-719","consensus_level":"medium","plddt":90.776,"start":667,"end":719}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16799","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q16799-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q16799-F1-predicted_aligned_error_v6.png","plddt_mean":48.09},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RTN1","jax_strain_url":"https://www.jax.org/strain/search?query=RTN1"},"sequence":{"accession":"Q16799","fasta_url":"https://rest.uniprot.org/uniprotkb/Q16799.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q16799/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16799"}},"corpus_meta":[{"pmid":"28981095","id":"PMC_28981095","title":"RTN1-C mediates cerebral ischemia/reperfusion injury via ER stress and mitochondria-associated apoptosis pathways.","date":"2017","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/28981095","citation_count":216,"is_preprint":false},{"pmid":"26227493","id":"PMC_26227493","title":"RTN1 mediates progression of kidney disease by inducing ER stress.","date":"2015","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/26227493","citation_count":84,"is_preprint":false},{"pmid":"19140693","id":"PMC_19140693","title":"Nucleic acid binding of the RTN1-C C-terminal region: toward the functional role of a reticulon protein.","date":"2009","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19140693","citation_count":38,"is_preprint":false},{"pmid":"28733667","id":"PMC_28733667","title":"RTN1 and RTN3 protein are differentially associated with senile plaques in Alzheimer's brains.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28733667","citation_count":36,"is_preprint":false},{"pmid":"22798490","id":"PMC_22798490","title":"Integrity and function of the Saccharomyces cerevisiae spindle pole body depends on connections between the membrane proteins Ndc1, Rtn1, and Yop1.","date":"2012","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22798490","citation_count":24,"is_preprint":false},{"pmid":"17303085","id":"PMC_17303085","title":"Two hydrophobic segments of the RTN1 family determine the ER localization and retention.","date":"2007","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/17303085","citation_count":14,"is_preprint":false},{"pmid":"20000484","id":"PMC_20000484","title":"Reticulon RTN1-C(CT) peptide: a potential nuclease and inhibitor of histone deacetylase enzymes.","date":"2010","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20000484","citation_count":12,"is_preprint":false},{"pmid":"34062006","id":"PMC_34062006","title":"LncRNA TUG1 ameliorates diabetic nephropathy via inhibition of PU.1/RTN1 signaling pathway.","date":"2021","source":"Journal of leukocyte biology","url":"https://pubmed.ncbi.nlm.nih.gov/34062006","citation_count":11,"is_preprint":false},{"pmid":"25543119","id":"PMC_25543119","title":"Identification of MANF as a protein interacting with RTN1-C.","date":"2014","source":"Acta biochimica et biophysica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/25543119","citation_count":8,"is_preprint":false},{"pmid":"31002913","id":"PMC_31002913","title":"RTN1-C is involved in high glucose-aggravated neuronal cell subjected to oxygen-glucose deprivation and reoxygenation injury via endoplasmic reticulum stress.","date":"2019","source":"Brain research bulletin","url":"https://pubmed.ncbi.nlm.nih.gov/31002913","citation_count":7,"is_preprint":false},{"pmid":"33372676","id":"PMC_33372676","title":"RTN1-C mediates cerebral ischemia/reperfusion injury via modulating autophagy.","date":"2021","source":"Acta biochimica et biophysica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/33372676","citation_count":7,"is_preprint":false},{"pmid":"34607459","id":"PMC_34607459","title":"Spindle Dynamics during Meiotic Development of the Fungus Podospora anserina Requires the Endoplasmic Reticulum-Shaping Protein RTN1.","date":"2021","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/34607459","citation_count":5,"is_preprint":false},{"pmid":"35747917","id":"PMC_35747917","title":"[The Expression of RTN1 in Lung Adenocarcinoma and 
Its Effect on Immune Microenvironment].","date":"2022","source":"Zhongguo fei ai za zhi = Chinese journal of lung cancer","url":"https://pubmed.ncbi.nlm.nih.gov/35747917","citation_count":4,"is_preprint":false},{"pmid":"30521940","id":"PMC_30521940","title":"Downregulation of RTN1-C attenuates MPP+-induced neuronal injury through inhibition of mGluR5 pathway in SN4741 cells.","date":"2018","source":"Brain research bulletin","url":"https://pubmed.ncbi.nlm.nih.gov/30521940","citation_count":4,"is_preprint":false},{"pmid":"30352262","id":"PMC_30352262","title":"Knockdown of RTN1-C attenuates traumatic neuronal injury through regulating intracellular Ca2+ homeostasis.","date":"2018","source":"Neurochemistry international","url":"https://pubmed.ncbi.nlm.nih.gov/30352262","citation_count":3,"is_preprint":false},{"pmid":"22522967","id":"PMC_22522967","title":"A metal-binding site in the RTN1-C protein: new perspectives on the physiological role of a neuronal protein.","date":"2012","source":"Metallomics : integrated biometal science","url":"https://pubmed.ncbi.nlm.nih.gov/22522967","citation_count":3,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10312,"output_tokens":2794,"usd":0.036423,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10083,"output_tokens":3979,"usd":0.074945,"stage2_stop_reason":"end_turn"},"total_usd":0.111368,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"RTN1A interacts with PERK (an ER stress sensor) through its N-terminal and C-terminal domains; mutation of these domains prevents RTN1A-induced ER stress, establishing that RTN1A drives ER stress and apoptosis via direct physical interaction with PERK.\",\n      \"method\": \"Co-immunoprecipitation, domain deletion/mutation analysis, in vitro overexpression and knockdown with ER stress marker readouts\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal interaction mapping with domain mutants, in vivo knockdown rescue, replicated across cell and mouse models in a single rigorous study\",\n      \"pmids\": [\"26227493\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"RTN1-C interacts with Bcl-xL and increases its localization in the ER, thereby reducing the anti-apoptotic activity of Bcl-xL and promoting mitochondria-associated apoptosis during ischemia/reperfusion injury.\",\n      \"method\": \"Co-immunoprecipitation, subcellular fractionation, RTN1-C overexpression/knockdown with apoptosis readouts in OGD/R and MCAO models\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus in vivo KD with defined phenotypic readout, single lab\",\n      \"pmids\": [\"28981095\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"ER localization of RTN1-A is determined by its two long hydrophobic segments in the C-terminal domain; each hydrophobic segment is individually sufficient for ER targeting, and the length of the hydrophobic segment contributes to ER retention versus Golgi localization.\",\n      \"method\": \"EGFP fusion constructs with deletion mutants and truncations, fluorescence microscopy\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with systematic deletion mutants, single lab, two constructs tested\",\n      \"pmids\": [\"17303085\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The C-terminal region of RTN1-C (residues 186–208) contains a consensus sequence homologous to H4 histone and binds and condenses nucleic acids; this binding activity is regulated by an acetylation-deacetylation mechanism via HDAC8, which deacetylates an acetylated form of the RTN1-C C-terminal peptide.\",\n      \"method\": \"Electrophoretic mobility shift assay, NMR/fluorescence spectroscopy, kinetic enzyme assay with HDAC8 and acetylated synthetic peptide\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical assays with synthetic peptide and mutagenesis-equivalent acetylated form, single lab\",\n      \"pmids\": [\"19140693\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The RTN1-C C-terminal peptide (residues 186–208) binds copper and nickel ions via an ATCUN motif; the resulting metal-peptide complexes exhibit nuclease activity and, in acetylated form, inhibit HDAC activity at micromolar concentrations.\",\n      \"method\": \"UV-vis spectroscopy, kinetic nuclease assay, HDAC enzymatic inhibition assay with metal-peptide complexes\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assays with defined metal complexes and acetylated peptide, single lab replicate of prior finding\",\n      \"pmids\": [\"20000484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The C-terminal region of RTN1-C contains a metal ion binding motif (HxE/D) capable of binding metal ions, suggesting metal binding contributes to formation of RTN multiprotein complexes.\",\n      \"method\": \"UV-vis spectroscopy, CD, multidimensional NMR spectroscopy, biological assays\",\n      \"journal\": \"Metallomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, biophysical characterization without functional reconstitution of complex formation\",\n      \"pmids\": [\"22522967\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"RTN1-C physically interacts with MANF (mesencephalic astrocyte-derived neurotrophic factor) in the ER; knockdown of RTN1-C reduces MANF localization in the ER.\",\n      \"method\": \"Yeast two-hybrid screen, GST pulldown, co-immunoprecipitation, immunofluorescence colocalization, RTN1-C knockdown\",\n      \"journal\": \"Acta biochimica et biophysica Sinica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interaction confirmed by orthogonal methods (Y2H, GST pulldown, Co-IP) plus localization consequence of KD, single lab\",\n      \"pmids\": [\"25543119\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"RTN1 deficiency in mice shows no obvious effect on BACE1 activity because RTN3 compensates by elevation; however, RTN1 is preferentially localized to dendrites (especially Purkinje cell dendrites) rather than axons, differentiating its subcellular distribution from RTN3.\",\n      \"method\": \"RTN1-null mouse generation, immunofluorescence, BACE1 activity assay, Western blot\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct KO mouse with defined functional assay (BACE1 activity) and subcellular localization, single lab\",\n      \"pmids\": [\"28733667\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RTN1-C knockdown inhibits surface expression of mGluR5 (but not mGluR1) and attenuates intracellular Ca2+ release in MPP+-treated SN4741 cells; the protective effect of RTN1-C knockdown is partially reversed by mGluR5 activation, placing RTN1-C upstream of mGluR5-mediated Ca2+ homeostasis.\",\n      \"method\": \"siRNA knockdown, Western blot for surface mGluR5, Ca2+ imaging, pharmacological mGluR5 activation\",\n      \"journal\": \"Brain research bulletin\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KD combined with pharmacological rescue and Ca2+ imaging, single lab, two orthogonal readouts\",\n      \"pmids\": [\"30521940\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RTN1-C knockdown protects cortical neurons from traumatic injury by inhibiting mGluR1-mediated ER Ca2+ release and suppressing STIM1-related store-operated Ca2+ entry (SOCE), thereby attenuating intracellular Ca2+ overload.\",\n      \"method\": \"siRNA knockdown, Ca2+ imaging, Western blot for STIM1, thapsigargin-induced SOCE assay\",\n      \"journal\": \"Neurochemistry international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with Ca2+ imaging and molecular target (STIM1) identification, single lab, multiple readouts\",\n      \"pmids\": [\"30352262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RTN1-C knockdown suppresses overactivated autophagy (reduced Beclin-1/PI-positive cells and autophagic protein expression) in ischemia/reperfusion injury models in vitro and in vivo, and reduces brain infarct volume after rapamycin treatment.\",\n      \"method\": \"Lentiviral shRNA knockdown, Western blot for autophagy markers, flow cytometry (Beclin-1/PI), MCAO rat model, rapamycin co-treatment\",\n      \"journal\": \"Acta biochimica et biophysica Sinica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo and in vitro KD with defined autophagy readouts, single lab\",\n      \"pmids\": [\"33372676\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In renal tubular epithelial cells under diabetic conditions, the transcription factor PU.1 binds the RTN1 promoter to drive RTN1 expression; lncRNA TUG1 inhibits PU.1 binding to the RTN1 promoter, thereby suppressing RTN1-mediated ER stress and apoptosis.\",\n      \"method\": \"Dual-luciferase reporter assay, RNA pulldown, RNA immunoprecipitation (RIP), chromatin immunoprecipitation (ChIP), adenoviral overexpression in vivo\",\n      \"journal\": \"Journal of leukocyte biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal chromatin and RNA interaction methods establishing transcriptional regulation of RTN1, single lab\",\n      \"pmids\": [\"34062006\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RTN1 (particularly its RTN1-C isoform) is an ER-resident membrane protein anchored by two hydrophobic transmembrane segments; it promotes ER stress by directly interacting with the PERK kinase via its N- and C-terminal domains, interacts with Bcl-xL to sequester it in the ER and reduce its anti-apoptotic function, modulates intracellular Ca2+ homeostasis through mGluR1/mGluR5 and STIM1-mediated store-operated entry, regulates autophagy flux, binds nucleic acids and HDAC enzymes via a C-terminal histone H4-like motif subject to acetylation control, and interacts with MANF in the ER, collectively placing RTN1-C as a multifunctional ER scaffold that amplifies apoptotic and stress signals in neurons and renal cells.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RTN1 is an endoplasmic reticulum membrane protein that functions as a pro-apoptotic stress amplifier in neurons and renal cells, coupling ER stress sensing to apoptosis, calcium dysregulation, and autophagy [#0, #1, #8]. Its ER localization is conferred by two long hydrophobic segments in the C-terminal domain, each individually sufficient for ER targeting, with segment length tuning ER retention versus Golgi distribution [#2]. RTN1A drives ER stress and apoptosis by binding the ER stress sensor PERK through its N- and C-terminal domains, an interaction required for RTN1-induced stress signaling [#0]. The RTN1-C isoform additionally engages the anti-apoptotic factor Bcl-xL, sequestering it in the ER to reduce its protective activity and promote mitochondria-associated apoptosis during ischemia/reperfusion [#1], and it interacts with the ER protein MANF, controlling MANF's ER localization [#6]. RTN1-C also governs intracellular Ca2+ homeostasis, acting upstream of mGluR5 surface expression and STIM1-mediated store-operated Ca2+ entry, such that its depletion attenuates Ca2+ overload and is protective in models of neuronal injury [#8, #9]. A C-terminal region (residues 186\\u2013208) bears a histone H4-like motif that binds and condenses nucleic acids under acetylation/deacetylation control by HDAC8 [#3]. RTN1-C depletion further suppresses overactivated autophagy in ischemia/reperfusion injury [#10], and RTN1 transcription is driven by PU.1 binding to its promoter, an event antagonized by lncRNA TUG1 to limit ER stress and apoptosis in diabetic renal tubular cells [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established what determines RTN1's subcellular address, showing the two C-terminal hydrophobic segments encode ER targeting and that segment length governs ER-versus-Golgi distribution.\",\n      \"evidence\": \"EGFP fusion constructs with deletion/truncation mutants analyzed by fluorescence microscopy\",\n      \"pmids\": [\"17303085\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Does not define a topology model for the full-length protein\", \"Functional consequence of Golgi mislocalization untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identified a histone H4-like motif in the RTN1-C C-terminus that binds and condenses nucleic acids and is reversibly regulated by HDAC8-mediated deacetylation, suggesting a chromatin-linked activity beyond membrane functions.\",\n      \"evidence\": \"EMSA, NMR/fluorescence spectroscopy, and kinetic enzyme assay with HDAC8 and synthetic acetylated peptide\",\n      \"pmids\": [\"19140693\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"In vitro peptide assays only; no demonstration of nuclear function in cells\", \"Physiological nucleic acid targets unknown\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Extended the C-terminal peptide characterization by showing it binds copper/nickel via an ATCUN motif, conferring nuclease activity and HDAC inhibition, linking metal coordination to its biochemical activities.\",\n      \"evidence\": \"UV-vis spectroscopy, kinetic nuclease assay, and HDAC inhibition assay with metal-peptide complexes\",\n      \"pmids\": [\"20000484\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"In vitro only; cellular relevance of metal binding not shown\", \"No reconstitution in full-length protein\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Biophysically characterized an HxE/D metal ion binding motif in the C-terminal region as a potential mediator of RTN multiprotein complex formation.\",\n      \"evidence\": \"UV-vis, CD, and multidimensional NMR spectroscopy\",\n      \"pmids\": [\"22522967\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No functional reconstitution of complex formation\", \"Single-lab biophysical characterization without in vivo support\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined an ER protein partner for RTN1-C by showing it physically interacts with MANF and controls MANF's ER localization, embedding RTN1-C in ER protein networks.\",\n      \"evidence\": \"Yeast two-hybrid, GST pulldown, Co-IP, immunofluorescence colocalization, and knockdown\",\n      \"pmids\": [\"25543119\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Functional consequence of the RTN1-C/MANF interaction unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Provided the central mechanism for RTN1-driven ER stress by mapping a direct PERK interaction to the N- and C-terminal domains and showing domain mutation abolishes RTN1-induced ER stress and apoptosis.\",\n      \"evidence\": \"Co-IP, domain deletion/mutation analysis, and overexpression/knockdown with ER stress readouts in cell and mouse models\",\n      \"pmids\": [\"26227493\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Whether RTN1 modulates the other ER stress arms (IRE1, ATF6) not addressed\", \"Stoichiometry and structural basis of the PERK interaction unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected RTN1-C to mitochondrial apoptosis by showing it binds Bcl-xL and increases its ER localization, reducing its anti-apoptotic activity during ischemia/reperfusion.\",\n      \"evidence\": \"Co-IP, subcellular fractionation, and overexpression/knockdown with apoptosis readouts in OGD/R and MCAO models\",\n      \"pmids\": [\"28981095\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Direct versus indirect nature of Bcl-xL sequestration not fully resolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Distinguished RTN1 from its paralog RTN3 in vivo, showing RTN1 loss does not impair BACE1 activity due to RTN3 compensation and that RTN1 is preferentially dendritic.\",\n      \"evidence\": \"RTN1-null mouse, immunofluorescence, BACE1 activity assay, and Western blot\",\n      \"pmids\": [\"28733667\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Dendritic function of RTN1 not defined\", \"Phenotype masked by RTN3 redundancy\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Established RTN1-C as a regulator of neuronal Ca2+ homeostasis, placing it upstream of mGluR5 surface expression and STIM1-mediated store-operated Ca2+ entry, with knockdown protecting neurons from Ca2+ overload.\",\n      \"evidence\": \"siRNA knockdown, Ca2+ imaging, surface mGluR5/STIM1 Western blots, pharmacological mGluR5 activation, and thapsigargin SOCE assay in MPP+ and traumatic injury models\",\n      \"pmids\": [\"30521940\", \"30352262\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Mechanism by which RTN1-C controls mGluR5 surface trafficking unknown\", \"Receptor selectivity (mGluR5 vs mGluR1) across models not reconciled\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Broadened RTN1-C's stress repertoire to autophagy, showing its knockdown suppresses overactivated autophagy and reduces infarct volume in ischemia/reperfusion models.\",\n      \"evidence\": \"Lentiviral shRNA knockdown, autophagy marker Western blots, flow cytometry, MCAO rat model with rapamycin co-treatment\",\n      \"pmids\": [\"33372676\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Molecular link between RTN1-C and the autophagy machinery undefined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined transcriptional control of RTN1, showing PU.1 activates the RTN1 promoter and lncRNA TUG1 antagonizes this to suppress RTN1-mediated ER stress and apoptosis in diabetic renal tubular cells.\",\n      \"evidence\": \"Dual-luciferase reporter, RNA pulldown, RIP, ChIP, and adenoviral overexpression in vivo\",\n      \"pmids\": [\"34062006\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Whether this regulatory axis operates in neuronal tissues untested\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the membrane-anchored ER scaffold functions integrate with the C-terminal histone-like nucleic acid-binding/HDAC-modulating activity, and whether a single structural model reconciles RTN1's PERK, Bcl-xL, MANF, and Ca2+-regulatory roles, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No integrated structural model of full-length RTN1\", \"Cellular role of the nucleic acid-binding/metal-binding C-terminal motif undemonstrated\", \"Mechanistic unification of ER stress, Ca2+, and autophagy roles lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [8, 9]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1, 2, 6]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [1, 11]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PERK\", \"BCL2L1\", \"MANF\", \"STIM1\", \"HDAC8\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}